Add test for minimum dependencies #1573
Workflow file for this run
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| name: PyTest | |
| on: | |
| pull_request: | |
| jobs: | |
| get_dockerfiles: | |
| name: Get list of dockerfiles for different containers | |
| runs-on: ubuntu-latest | |
| permissions: | |
| packages: read | |
| outputs: | |
| imagenames: ${{ steps.set-matrix.outputs.imagenames }} | |
| steps: | |
| - id: set-matrix | |
| env: | |
| GH_TOKEN: ${{ secrets.GHCR_TOKEN }} | |
| run: | | |
| imagenames=$(curl -s --request GET \ | |
| --url "https://api.github.com/orgs/PTB-MR/packages?package_type=container" \ | |
| --header "Authorization: Bearer $GH_TOKEN" | jq -r '.[].name') | |
| echo "image names: $imagenames" | |
| imagenames_latest=() | |
| for image in $(echo $imagenames) | |
| do | |
| echo "checking $image ..." | |
| if docker manifest inspect "ghcr.io/ptb-mr/"$image":latest" >/dev/null; then | |
| echo "... $image added" | |
| imagenames_latest+=$image":" | |
| fi | |
| done | |
| echo "image names with tag latest: $imagenames_latest" | |
| imagenames_latest=$(echo $imagenames_latest | jq -R -c 'split(":")[:-1]') | |
| echo "image names with tag latest: $imagenames_latest" | |
| echo "imagenames=$imagenames_latest" >> $GITHUB_OUTPUT | |
| - name: Dockerfile overview | |
| run: | | |
| echo "final list of images with tag latest: ${{ steps.set-matrix.outputs.imagenames }}" | |
| test: | |
| name: Run tests and get coverage report | |
| needs: get_dockerfiles | |
| runs-on: ubuntu-latest | |
| permissions: | |
| pull-requests: write | |
| contents: write | |
| strategy: | |
| matrix: | |
| imagename: ${{ fromJson(needs.get_dockerfiles.outputs.imagenames) }} | |
| # runs within Docker container | |
| container: | |
| image: ghcr.io/ptb-mr/${{ matrix.imagename }}:latest | |
| options: --user runner | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: Install mrpro and dependencies | |
| run: pip install --upgrade --upgrade-strategy "eager" .[test] | |
| - name: Install pytest-github-actions-annotate-failures plugin | |
| run: pip install pytest-github-actions-annotate-failures | |
| - name: Run PyTest | |
| run: | | |
| pytest -n 4 -m "not cuda" --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=mrpro | tee pytest-coverage.txt | |
| - name: Check for pytest.xml | |
| run: | | |
| if [ -f pytest.xml ]; then | |
| echo "pytest.xml file found. Continuing..." | |
| else | |
| echo "pytest.xml file not found. Please check previous 'Run PyTest' section for errors." | |
| exit 1 | |
| fi | |
| - name: Pytest coverage comment | |
| id: coverageComment | |
| uses: MishaKav/[email protected] | |
| with: | |
| pytest-coverage-path: ./pytest-coverage.txt | |
| junitxml-path: ./pytest.xml | |
| - name: Create the Badge | |
| uses: schneegans/[email protected] | |
| with: | |
| auth: ${{ secrets.GIST_SECRET }} | |
| gistID: 48e334a10caf60e6708d7c712e56d241 | |
| filename: coverage.json | |
| label: Coverage Report | |
| message: ${{ steps.coverageComment.outputs.coverage }} | |
| color: ${{ steps.coverageComment.outputs.color }} | |
| namedLogo: python | |
| - name: Set pipeline status | |
| if: steps.coverageComment.outputs.errors != 0 || steps.coverageComment.outputs.failures != 0 | |
| uses: actions/github-script@v7 | |
| with: | |
| script: | | |
| core.setFailed('PyTest workflow failed with ${{ steps.coverageComment.outputs.errors }} errors and ${{ steps.coverageComment.outputs.failures }} failures.') | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| # Cancel in-progress runs when a new workflow with the same group name is triggered | |
| cancel-in-progress: true |